Evidence map›Paper›PMID 27459886›Full record

ArticleVirus genes2016

Review of Beet pseudoyellows virus genome structure built the consensus genome organization of cucumber strains and highlighted the unique feature of strawberry strain.

Md Shamim Akhter, Sachin Ashok Bhor, Ngcebo Hlalele, Masahiro Nao, Ken-Taro Sekine, Takashi Yaeno, Naoto Yamaoka, Masamichi Nishiguchi, Augustine Gubba, Kappei Kobayashi

Abstract read
PubMed Publisher
In one paragraph

Article in Virus genes, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
1.4field-weighted citation impact, top 12% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 6 citations in OpenAlex.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 5 institutions in 3 countries.

Md Shamim AkhterLaboratory of Plant Molecular Biology and Virology, Faculty of Agriculture, The United Graduate School of Agricultural Sciences, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan.
Sachin Ashok BhorLaboratory of Plant Molecular Biology and Virology, Faculty of Agriculture, The United Graduate School of Agricultural Sciences, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan.
Ngcebo HlaleleDepartment of Plant Pathology, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa.
Masahiro NaoEhime Prefecture Plant Protection Office, Matsuyama, Ehime, 790-2405, Japan.
Ken-Taro SekineIwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan.
Takashi YaenoLaboratory of Plant Molecular Biology and Virology, Faculty of Agriculture, The United Graduate School of Agricultural Sciences, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan.
Naoto YamaokaLaboratory of Plant Molecular Biology and Virology, Faculty of Agriculture, The United Graduate School of Agricultural Sciences, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan.
Masamichi NishiguchiLaboratory of Plant Molecular Biology and Virology, Faculty of Agriculture, The United Graduate School of Agricultural Sciences, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan.
Augustine GubbaDepartment of Plant Pathology, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa.
Kappei KobayashiLaboratory of Plant Molecular Biology and Virology, Faculty of Agriculture, The United Graduate School of Agricultural Sciences, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan. kappei@ehime-u.ac.jp.
Ehime University · JPUniversity of KwaZulu-Natal · ZABangladesh Agricultural Research Institute · BDEhime Prefectural Education Center · JPUniversity of the Ryukyus University Hospital · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The complete nucleotide sequences of Beet pseudoyellows virus (BPYV)-MI (cucumber isolate; Matsuyama, Idai) genomic RNAs 1 and 2 were determined and compared with the previously sequenced Japanese cucumber strain (BPYV-JC) and a strawberry strain (BPYV-S). The RNA 2 of BPYV-MI showed 99 % nucleotide sequence identity with both BPYV-JC and -S having highly conserved eight ORFs. In contrast, the RNA1 of BPYV-MI showed sequence identities of 98 and 86 % with BPYV-JC and -S, respectively. Phylogenetic analysis of RNA-dependent RNA polymerase (RdRp) coding sequences from three fully sequenced BPYV strains and five partially sequenced cucurbit-infecting BPYV strains from Japan and South Africa has shown that cucurbit-infecting strains are closer to each other than to BPYV-S. In addition, the strawberry strain BPYV-S has an ORF2 in the downstream of RdRp gene in RNA1, but all the cucumber strains, BPYV-JC, -MI, and those from South Africa, lacked the ORF2 of RNA1, highlighting the difference between common BPYV cucumber strains and a unique strawberry strain.

Indexed as

Genome, ViralGenomicsCrinivirusCucumis sativusFragariaHost-Pathogen InteractionsOpen Reading FramesPhylogenyPlant DiseasesSequence Analysis, RNABPYVCrinivirusCucumberHost adaptationStrawberry

Identifiers

PMID27459886
OpenAlexW2496804172

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.